Under the non-exclusive tag (worth $14,599,000) the Bears opted to use, Jeffery is allowed to negotiate with other teams. If he signs with a different team, that team will owe the Bears two first-round draft picks in compensation.
Talks between the Bears and Jeffery regarding the framework for a long-term deal continue, a source told ESPN's Josina Anderson.
"I'll continue to be patient and see how things work out," Jeffery told Anderson.
The team had until 4 p.m. ET Tuesday to use its franchise or transition tag on Jeffery. ESPN's Adam Schefter previously reported the Bears would use the franchise tag on Jeffery if the team couldn't sign him to an extension before the deadline.
The sides have until July 15 to try to reach a long-term deal.
Last week, Bears general manager Ryan Pace confirmed at the combine that the team was in talks with Jeffery to try to retain him, but placing the franchise tag on him was an option.
Jeffery appeared in just nine games last season thanks to a variety of ailments that began in training camp, when he suffered a serious calf strain in a closed walk-through practice before Chicago's preseason opener. He missed all four exhibition games, then was shut down in December with a hamstring injury after having played in just nine regular-season games.
When healthy, Jeffery is one of the Bears' top players on offense. He caught 54 passes for 807 yards and four touchdowns this past season. He also tied a franchise record with three straight 100-yard receiving games against Detroit, Minnesota and San Diego.
Jeffery, 26, currently has a dozen 100-yard receiving games in his four seasons with the Bears, tied for fifth most in franchise history. He set career highs with 89 catches for 1,421 yards in 2013. The second-round pick out of South Carolina also hauled in 10 touchdown catches in 2014.
ESPN Bears reporter Jeff Dickerson contributed to this report.